Welcome to rdeval’s documentation!
rdeval is a tool to efficiently generate and visualize summary statistics for sequence data.
Check out the Usage section for further information, including how to installation the project. A description of rdeval’s .rd file format can be found in the format specification section.
Note
rdeval’s source code is available here.
Contents
- Usage
- Installation
- Useful commands
- Help and Usage:
- Output size list, based on unsorted (‘u’), sorted (‘s’), histogram (‘h’) or inverse cumulative table (‘c’) [-s/–out-size]:
- To generate a read summary:
- To generate stats:
- To obtain a distribution of quality for each read (q) or both length and quality(a):
- To generate a per-read report:
- To filter the reads to be assessed, by length (‘l’) or quality (‘q’), or both:
- To exclude data from analysis, based on read header information in a list [-e/–exclude-list]:
- To include data in the analysis, based on read header information in a list [-i/include-list]:
- To write reads to a file or generate an rd summary file (output options: fa*[.gz], bam, cram, rd):
- To compress all the homopolymers longer than ‘n’ in the input:
- To subsample reads (requires an float between 0 and 1):
- To make subsampling reproducible, use the ‘–random-seed <int>’ option:
- To print md5 of a .rd file:
- To output data to a .rd file, then to run rdeval on the .rd file:
- This can also be done on multiple files in parallel, combining the results at the end:
- To read a .bam or .cram file:
- To display the software version number [-v/–version]:
- Generation of .rd reports
- PacBio CiFi reads
- Rdeval snapshot format specification
- Memory usage and parallel processing